Zafgen - p1068

Jennifer Rohn

doi:10.1038/nbt1211-1068

Zafgen hopes that small-molecule targeting of methionine aminopeptidase 2 (MetAP2), an enzyme originally associated with tumor angiogenesis, will lead to a new anti-obesity drug.

Abstract - | Full Text - Zafgen | PDF (129 KB) - Zafgen

Generation of the potent anti-malarial drug artemisinin in tobacco - pp1072 - 1074

Moran Farhi, Elena Marhevka, Julius Ben-Ari, Anna Algamas-Dimantov, Zhuobin Liang, Vardit Zeevi, Orit Edelbaum, Ben Spitzer-Rimon, Hagai Abeliovich, Betty Schwartz, Tzvi Tzfira & Alexander Vainstein

doi:10.1038/nbt.2054

Full Text - Generation of the potent anti-malarial drug artemisinin in tobacco | PDF (410 KB) - Generation of the potent anti-malarial drug artemisinin in tobacco | Supplementary information

Relative potential of biosynthetic pathways for biofuels and bio-based products - pp1074 - 1078

Deepak Dugar & Gregory Stephanopoulos

doi:10.1038/nbt.2055

Full Text - Relative potential of biosynthetic pathways for biofuels and bio-based products | PDF (346 KB) - Relative potential of biosynthetic pathways for biofuels and bio-based products | Supplementary information

Re-evaluating PARP1 inhibitor in cancer - pp1078 - 1079

Alexei Tulin

doi:10.1038/nbt.2058

Full Text - Re-evaluating PARP1 inhibitor in cancer | PDF (293 KB) - Re-evaluating PARP1 inhibitor in cancer

Access to human embryonic stem cell lines - pp1079 - 1081

Aaron D Levine

doi:10.1038/nbt.2029

Full Text - Access to human embryonic stem cell lines | PDF (285 KB) - Access to human embryonic stem cell lines | Supplementary information

Sarbanes-Oxley overburdens biotech companies - pp1081 - 1082

Mark Kessel

doi:10.1038/nbt.2059

Full Text - Sarbanes-Oxley overburdens biotech companies | PDF (166 KB) - Sarbanes-Oxley overburdens biotech companies

Agricultural microbial resources: private property or global commons? - pp1091 - 1093

David Kothamasi, Matthew Spurlock & E Toby Kiers

doi:10.1038/nbt.2056

Agricultural microbes have become an attractive target for patenting, but the lack of a consistent global patent regime and increasingly heated debates over microbial ownership rights are barriers to the development of this resource.

Abstract - | Full Text - Agricultural microbial resources: private property or global commons? | PDF (152 KB) - Agricultural microbial resources: private property or global commons?

Recent patent applications related to agricultural microbes - p1094

doi:10.1038/nbt.2066

Full Text - Recent patent applications related to agricultural microbes | PDF (48 KB) - Recent patent applications related to agricultural microbes

DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes - pp1103 - 1108

Subhajyoti De & Franziska Michor

doi:10.1038/nbt.2030

Copy-number changes in cancer genomes may be caused by errors during the replication of colocalized DNA regions. De and Michor provide genome-wide evidence for this model by integrating data on DNA replication timing, the three-dimensional organization of the genome and copy-number alterations in cancer.

Abstract - | Full Text - DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes | PDF (778 KB) - DNA replication timing and long-range DNA interactions predict mutational landscapes of cancer genomes | Supplementary information

See also: News and Views by Hastings & Rosenberg

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer - pp1109 - 1113

Geoff Fudenberg, Gad Getz, Matthew Meyerson & Leonid A Mirny

doi:10.1038/nbt.2049

Copy-number changes, point mutations and rearrangements are all usually found in cancer genomes, but their relative frequencies are highly variable. Using statistical approaches to model different processes, Fudenberg et al. find that copy number gain and loss is influenced by the three-dimensional organization of the genome in the nucleus.

Abstract - | Full Text - High order chromatin architecture shapes the landscape of chromosomal alterations in cancer | PDF (628 KB) - High order chromatin architecture shapes the landscape of chromosomal alterations in cancer | Supplementary information

See also: News and Views by Hastings & Rosenberg

In silico feedback for in vivo regulation of a gene expression circuit - pp1114 - 1116

Andreas Milias-Argeitis, Sean Summers, Jacob Stewart-Ornstein, Ignacio Zuleta, David Pincus, Hana El-Samad, Mustafa Khammash & John Lygeros

doi:10.1038/nbt.2018

Creating synthetic biological circuits can be maddeningly difficult because of unpredictable stimuli and unknown variability in the system. Milias-Argeitis et al. circumvent these problems by moving control functions outside the cell—to a computer—and connecting computer and cell through optogenetics.

Abstract - | Full Text - In silico feedback for in vivo regulation of a gene expression circuit | PDF (303 KB) - In silico feedback for in vivo regulation of a gene expression circuit | Supplementary information

Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells - pp1117 - 1119

Kitai Kim, Rui Zhao, Akiko Doi, Kitwa Ng, Juli Unternaehrer, Patrick Cahan, Huo Hongguang, Yuin-Han Loh, Martin J Aryee, M William Lensch, Hu Li, James J Collins, Andrew P Feinberg & George Q Daley

doi:10.1038/nbt.2052

Mouse induced pluripotent stem (iPS) cells have been shown to retain an epigenetic 'memory' of their cell type of origin. Kim et al. study this question in human cells and document both incomplete erasure of methylation and aberrant de novo methylation during reprogramming.

Abstract - | Full Text - Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells | PDF (357 KB) - Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells | Supplementary information

Single-cell dissection of transcriptional heterogeneity in human colon tumors - pp1120 - 1127

Piero Dalerba, Tomer Kalisky, Debashis Sahoo, Pradeep S Rajendran, Michael E Rothenberg, Anne A Leyrat, Sopheak Sim, Jennifer Okamoto, Darius M Johnston, Dalong Qian, Maider Zabala, Janet Bueno, Norma F Neff, Jianbin Wang, Andrew A Shelton, Brendan Visser, Shigeo Hisamori, Yohei Shimono, Marc van de Wetering, Hans Clevers, Michael F Clarke & Stephen R Quake

doi:10.1038/nbt.2038

Not all cells in a tumor are alike, but our ability to characterize cancer heterogeneity in detail has been limited. Dalerba et al. use high-throughput single-cell expression analysis to define clinically relevant subpopulations in normal and cancerous colon tissue.

Abstract - | Full Text - Single-cell dissection of transcriptional heterogeneity in human colon tumors | PDF (2,704 KB) - Single-cell dissection of transcriptional heterogeneity in human colon tumors | Supplementary information

See also: News and Views by Dornan & Settleman

Efficacy of genetically modified Bt toxins against insects with different genetic mechanisms of resistance - pp1128 - 1131

Bruce E Tabashnik, Fangneng Huang, Mukti N Ghimire, B Rogers Leonard, Blair D Siegfried, Murugesan Rangasamy, Yajun Yang, Yidong Wu, Linda J Gahan, David G Heckel, Alejandra Bravo & Mario Soberón

doi:10.1038/nbt.1988

The benefits of crops that produce insecticidal toxins from Bacillus thuringiensis (Bt) are threatened by the emergence of insect resistance. Working with five major crop pests, Tabashnik et al. show that previously described variant Bt toxins kill pests rendered resistant to native Bt toxins by multiple mechanisms.

First Paragraph - | Full Text - Efficacy of genetically modified Bt toxins against insects with different genetic mechanisms of resistance | PDF (448 KB) - Efficacy of genetically modified Bt toxins against insects with different genetic mechanisms of resistance | Supplementary information

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage - pp1132 - 1144

Katherine Amps, Peter W Andrews, George Anyfantis, Lyle Armstrong, Stuart Avery, Hossein Baharvand, Julie Baker, Duncan Baker, Maria B Munoz, Stephen Beil, Nissim Benvenisty, Dalit Ben-Yosef, Juan-Carlos Biancotti, Alexis Bosman, Romulo Martin Brena, Daniel Brison, Gunilla Caisander, María V Camarasa, Jieming Chen, Eric Chiao, Young Min Choi, Andre B H Choo, Daniel Collins, Alan Colman, Jeremy M Crook, George Q Daley, Anne Dalton, Paul A De Sousa, Chris Denning, Janet Downie, Petr Dvorak, Karen D Montgomery, Anis Feki, Angela Ford, Victoria Fox, Ana M Fraga, Tzvia Frumkin, Lin Ge, Paul J Gokhale, Tamar Golan-Lev, Hamid Gourabi, Michal Gropp, Lu Guangxiu, Ales Hampl, Katie Harron, Lyn Healy, Wishva Herath, Frida Holm, Outi Hovatta, Johan Hyllner, Maneesha S Inamdar, Astrid Kresentia Irwanto, Tetsuya Ishii, Marisa Jaconi, Ying Jin, Susan Kimber, Sergey Kiselev, Barbara B Knowles, Oded Kopper, Valeri Kukharenko, Anver Kuliev, Maria A Lagarkova, Peter W Laird, Majlinda Lako, Andrew L Laslett, Neta Lavon, Dong Ryul Lee, Jeoung Eun Lee, Chunliang Li, Linda S Lim, Tenneille E Ludwig, Yu Ma, Edna Maltby, Ileana Mateizel, Yoav Mayshar, Maria Mileikovsky, Stephen L Minger, Takamichi Miyazaki, Shin Yong Moon, Harry Moore, Christine Mummery, Andras Nagy, Norio Nakatsuji, Kavita Narwani, Steve K W Oh, Sun Kyung Oh, Cia Olson, Timo Otonkoski, Fei Pan, In-Hyun Park, Steve Pells, Martin F Pera, Lygia V Pereira, Ouyang Qi, Grace Selva Raj, Benjamin Reubinoff, Alan Robins, Paul Robson, Janet Rossant, Ghasem H Salekdeh, Thomas C Schulz, Karen Sermon, Jameelah Sheik Mohamed, Hui Shen, Eric Sherrer, Kuldip Sidhu, Shirani Sivarajah, Heli Skottman, Claudia Spits, Glyn N Stacey, Raimund Strehl, Nick Strelchenko, Hirofumi Suemori, Bowen Sun, Riitta Suuronen, Kazutoshi Takahashi, Timo Tuuri, Parvathy Venu, Yuri Verlinsky, Dorien Ward-van Oostwaard, Daniel J Weisenberger, Yue Wu, Shinya Yamanaka, Lorraine Young, Qi Zhou & The International Stem Cell Initiative

doi:10.1038/nbt.2051

The International Stem Cell Initiative compares 125 ethnically diverse human embryonic stem cell lines at early and late passage. Data on karotype, single-nucleotide polymorphisms and methylation shed light on how the cells adapt to long-term culture.

Abstract - | Full Text - Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage | PDF (1,173 KB) - Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage | Supplementary information

People - p1150

doi:10.1038/nbt.2067

Full Text - People | PDF (100 KB) - People